Epigenetic metaphors: an interdisciplinary translation of encoding and decoding

Looking at the new and often disputed science of epigenetics, we examined the challenges faced by scientists when they communicate scientific research to the public. We focused on the use of metaphors to illustrate notions of epigenetics and genetics. We studied the “encoding” by epigeneticists and “decoding” in focus groups with diverse backgrounds. We observed considerable overlap in the dominant metaphors favored by both researchers and the lay public. However, the groups differed markedly in their interpretations of which metaphors aided understanding or not. We conclude by discussing the role of metaphors and their interpretations in the context of a shift from pre-deterministic genomic metaphors to more active, dynamic and nuanced epigenetic metaphors. These reflections on the choice of metaphors and differences in encoding/decoding are important for science communication and scientific boundary-maintenance.     

Epigenetic determinism in science and society

The epigenetic “revolution” in science cuts across many disciplines, and it is now one of the fastest-growing research areas in biology. Increasingly, claims are made that epigenetics research represents a move away from the genetic determinism that has been prominent both in biological research and in understandings of the impact of biology on society. We discuss to what extent an epigenetic framework actually supports these claims. We show that, in contrast to the received view, epigenetics research is often couched in language as deterministic as genetics research in both science and the popular press. We engage the rapidly emerging conversation about the impact of epigenetics on public discourse and scientific practice, and we contend that the notion of epigenetic determinism – or the belief that epigenetic mechanisms determine the expression of human traits and behaviors – matters for understandings of the influence of biology and society on population health.     

Unpacking collaborative depression care: examining two essential tasks for implementation

Clinical guidelines recommend that assessment and management of patients with stroke commences early including in emergency departments (ED). To inform the development of an implementation intervention targeted in ED, we conducted a systematic review of qualitative and quantitative studies to identify relevant barriers and enablers to six key clinical behaviours in acute stroke care: appropriate triage, thrombolysis administration, monitoring and management of temperature, blood glucose levels, and of swallowing difficulties and transfer of stroke patients in ED. Studies of any design, conducted in ED, where barriers or enablers based on primary data were identified for one or more of these six clinical behaviours. Major biomedical databases (CINAHL, OVID SP EMBASE, OVID SP MEDLINE) were searched using comprehensive search strategies. The barriers and enablers were categorised using the theoretical domains framework (TDF). The behaviour change technique (BCT) that best aligned to the strategy each enabler represented was selected for each of the reported enablers using a standard taxonomy. Five qualitative studies and four surveys out of the 44 studies identified met the selection criteria. The majority of barriers reported corresponded with the TDF domains of “environmental, context and resources” (such as stressful working conditions or lack of resources) and “knowledge” (such as lack of guideline awareness or familiarity). The majority of enablers corresponded with the domains of “knowledge” (such as education for physicians on the calculated risk of haemorrhage following intravenous thrombolysis [tPA]) and “skills” (such as providing opportunity to treat stroke cases of varying complexity). The total number of BCTs assigned was 18. The BCTs most frequently assigned to the reported enablers were “focus on past success” and “information about health consequences.” Barriers and enablers for the delivery of key evidence-based protocols in an emergency setting have been identified and interpreted within a relevant theoretical framework. This new knowledge has since been used to select specific BCTs to implement evidence-based care in an ED setting. It is recommended that findings from similar future reviews adopt a similar theoretical approach. In particular, the use of existing matrices to assist the selection of relevant BCTs.     

The Dolezal affair: race,gender, and the micropolitics of identity

ABSTRACT

This article treats the pairing of “transgender” and “transracial” in the intertwined discussion of Caitlyn Jenner and Rachel Dolezal as an intellectual opportunity rather than a political provocation. I situate the Dolezal affair in the context of the massive destabilization of long taken-for-granted categorical frameworks, which has significantly enlarged the scope for choice and self-fashioning in the domains of race, ethnicity, sex, gender, and sexuality. Anxieties about opportunistic, exploitative, or fraudulent identity claims have generated efforts to “police” unorthodox claims – as well as efforts to defend such claims against policing – in the name of authentic, objective, and unchosen identities. Instead of a shift from given to chosen identities, as posited by theories of reflexive modernity, we see a sharpened tension between idioms of choice, autonomy, subjectivity, and self-fashioning on the one hand and idioms of givenness, essence, objectivity, and nature on the other.     

Learning a functional grammar of protein domains using natural language word embedding techniques

In this paper, using Word2vec, a widely-used natural language processing method, we demonstrate that protein domains may have a learnable implicit semantic “meaning” in the context of their functional contributions to the multi-domain proteins in which they are found. Word2vec is a group of models which can be used to produce semantically meaningful embeddings of words or tokens in a fixed-dimension vector space. In this work, we treat multi-domain proteins as “sentences” where domain identifiers are tokens which may be considered as “words.” Using all InterPro (Finn et al. 2017) pfam domain assignments we observe that the embedding could be used to suggest putative GO assignments for Pfam (Finn et al. 2016) domains of unknown function.     

Drawing Disability in Japanese Manga: Visual Politics, Embodied Masculinity, and Wheelchair Basketball in Inoue Takehiko’s REAL

This work explores disability in the cultural context of contemporary Japanese comics. In contrast to Western comics, Japanese manga have permeated the social fabric of Japan to the extent that vast numbers of people read manga on a daily basis. It has, in fact, become such a popular medium for visual communication that the Japanese government and education systems utilize manga as a social acculturation and teaching tool. This multibillion dollar industry is incredibly diverse, and one particularly popular genre is sports manga. However, Inoue Takehiko’s award-winning manga series REAL departs from more conventional sports manga, which typically focus on able-bodied characters with sometimes exaggerated superhuman physical abilities, by adopting a more realistic approach to the world of wheelchair basketball and the people who play it. At the same time REAL explores cultural attitudes toward disability in Japanese culture—where disability is at times rendered “invisible” either through accessibility problems or lingering associations of disability and shame. It is therefore extremely significant that manga, a visual medium, is rendering disability visible—the ultimate movement from margin to center. REAL devotes considerable attention to realistically illustrating the lived experiences of its characters both on and off the court. Consequently, the series not only educates readers about wheelchair basketball but also provides compelling insight into Japanese cultural notions about masculinity, family, responsibility, and identity. The basketball players—at first marginalized by their disability—join together in the unity of a sport typically characterized by its “abledness.”     

Racialization: a defense of the concept

This paper defends the concept of racialization against its critics. As the concept has become increasingly popular, questions about its meaning and value have been raised, and a backlash against its use has occurred. I argue that when “racialization” is properly understood, criticisms of the concept are unsuccessful. I defend a definition of racialization and identify its companion concept, “racialized group.” Racialization is often used as a synonym for “racial formation.” I argue that this is a mistake. Racial formation theory is committed to racial ontology, but racialization is best understood as the process through which racialized – rather than racial – groups are formed. “Racialization” plays a unique role in the conceptual landscape, and it is a key concept for race eliminativists and anti-realists about race.     

Moved to Dance: Remix,Rasa, and a New India

This article looks at Bollywood dance to explore the production of the commodified bodies of global consumer culture. It focuses on “embodiment” to examine how dominant sensibilities are altered through changes in dance training and technological innovations. I argue that analyzing the dancing body as a locus of experience and expression shifts the ground from culture as text or discourse (popular in postcolonial, poststructuralist or choreographic analysis) to embodiment of subjectivity. “Remix” is the term that describes both the new training techniques and the aesthetics of Indian dances. Since the older boundaries of high and low, classical and popular are fluid under globalization, “remix” is replacing traditional codes and aesthetic experiences associated with rasa. I draw on my fieldwork among the “background dancers” in Bollywood films to argue that as consumer culture creates the dominant mode of cultural expression in India, the only durable form of dance practice seems to be the practice of consumption.     

Ethnographic Note on Nation: Narratives and Symbols of the Early Post-socialist Nationalism in Lithuania

In the late 1980s and early 1990s Lithuania experienced the nationalist upheaval, which epitomized in the break up from the Soviet Union in 1990. Narratives and symbols were constitutive of the nationalist movement. “Nation” — the master symbol of that time — was reproduced in relation to the symbols of “the West,” and “the East,” as well as through the different values implied in “the West” and “the East” symbolism. Nationalist narratives reconstructed history and memory, reevaluated the present of the “reborn” nation, and drew the paths for the transition. Symbols and narratives were significant in mobilizing popular opinion, creating models for identity and action, and expressing moral and legitimate stances. They were a primary mechanism by which ideologies and cultural stances were shaped and maintained during the nationalist upheaval. In early 1990s the “nation” was redefined in the context of the Western tradition which was essential in communicating with the European countries and distancing from the former Soviet Union.     

Towards a metaphorical biology

The metaphorical nature of biological language is examined and the use of metaphors for providing the linguistic context in which similarities and differences are made is described. Certain pervasive metaphors which are characterised by systemic properties are noted, and in order to provide some focus to the study, systemic metaphors associated with machine, text and organism are discussed. Other systemic metaphors such as society and circuit are also reported. Some details concerning interrelations between automaton and organism are presented in the light of the previous discussion.An approach towards the analysis of biosystem metaphors is outlined which relates part-whole, organisational level and systemic metaphors in a single model. Examples are provided throughout the discussion and mainly come from computing. The potential for metaphorical transfers between these domains is considered.     

Xenophagy: A battlefield between host and microbe,and a possible avenue for cancer treatment

In eukaryotes, xenophagy is defined as a type of selective macroautophagy/autophagy that is used for eliminating invading pathogens. In contrast to other types of selective autophagy, such as mitophagy, pexophagy and ribophagy, xenophagy is used by eukaryotes for targeting microbes—hence the prefix “xeno” meaning “other” or “foreign”—that have infected a host cell, leading to their lysosomal degradation. This unique characteristic links xenophagy to antibacterial and antiviral defenses, as well as the immune response. Furthermore, recent studies suggest a complicated role of xenophagy in cancer, through either suppressing tumorigenesis or promoting survival of established tumors. In this issue, Sui et al. summarize previous and current studies of xenophagy and consider them in the context of anticancer treatment.     

From sequencing to annotating: extending the metaphor of the book of life from genetics to genomics

The article discusses how the metaphor of the Book of Life was extended over time to cover the life cycle of the Human Genome Project from genetics to genomics. In particular, the focus is on the role of extendable metaphors in the debate on the Human Genome Project in three European newspapers, popular scientific journals and scientific and scholarly articles from 1990 to 2002. In these different domains of use, various parts of the metaphor were highlighted. The metaphor of Book of Life was mainly used to justify the continuation of the gene research from gene sequencing to comparative genomics. Readily extendable metaphors, such as the Book of Life, function as useful communicative tools both over time and across domains of use.     

Women’s empowerment and rural revolution: rethinking “failed development”

One of the most frequently advanced explanations of the Maoists’ popularity in rural Nepal links dissatisfaction with the State to forms of consciousness and changes in expectations that are products and processes of development. Such theories often attribute popular support for the insurrection to frustrated desires stemming from “failed” or “incomplete” development. Against this, others suggest that it was the very “success” of empowerment programs which aimed to raise participants’ consciousness of oppression and its roots that inspired villagers to embrace revolutionary action. This paper argues that, despite their differences, both hypotheses reflect assumptions about gendered selfhood and political action that limit their recognition of what motivates Maoist sympathies. Extended research with women in Gorkha—a district where female support for the rebels is said to be especially strong—reveals that Gorkhali women’s support for the rebels is not inspired primarily by the desire for greater autonomy, choice or absolute liberation from social constraints, all of which ideals valorize a culturally specific vision of individual agency. Rather, women there report a sense of self that defines itself through social relations and commitments and which values the common good over individual self-interest, which they associate with an unjust state. The disjuncture between Gorkhali women’s own understandings of self and society and prevailing theories of what motivates people to rebel highlights the modernist assumptions that underlie—and potentially distort—otherwise diverse scholarly perspectives. Likewise, it implies that rebellions may be less about consciousness and more about morality than either “failed” or “successful” theories presume.     

甲基化敏感扩增多态性技术(MSAP)在生态学中的应用

DNA甲基化是生物体内最为重要的表观遗传修饰形式之一,在生态学上的应用越来越广泛。在收集、整理生态表观遗传学相关文献的基础上,介绍了甲基化敏感扩增多态性技术(MSAP)的原理、优势与局限性及其在生态学上的应用和展望。MSAP因其应用广泛、操作简便等优点成为研究DNA甲基化水平的有力工具,特别是在探究生物体如何快速适应生境变化以及外来入侵生物如何突破遗传瓶颈等问题上。MSAP技术能够很好地揭示生物种群内部或种群之间的表观遗传差异,是对遗传多样性、遗传变异研究的有力补充。     

Protectors,Aggressors, and Kinfolk: Dogs in a Tribal Community

Free-roaming dogs are a common phenomenon on many American Indian reservations as well as globally. Lack of canine restriction may be pathologized by outsiders, assumed to be a “problem” that reflects underlying individual or community dysfunction. Seldom investigated are the cultural logics underlying the lack of restriction, and the positive role that dogs may be playing in the community. This paper examines relationships between a northern plains reservation community and their dogs. We found these relationships to be complex and multifaceted, harkening back to a pre-contact past when human survival itself depended on the dog, and extending into a present shaped by a broad range of cultural notions about the human–dog relationship. We explore the concept of dog restriction, asking what it means for connections with dogs in a context where relationships with dogs run deep, but have been disrupted by settler colonialism. We found a community that very much desires dogs and views them positively, with their role as protector highly valued on nearly every level. While traditional notions guided many behaviors toward dogs, other conceptualizations were simultaneously in play, including rural ideas about animals as well as American popular culture. Our findings call into question the ethnocentric bias that construes all free-roaming dogs as strays, which is linked to cultural notions of “pet ownership” that equate love for dogs with restrictions on their movement.     

Being a burden to others and wishes to die: The importance of the sociopolitical context

All articles in May 2019’s special issue of Bioethics offer profound insights into the issue of “being a burden to others” in relation to wishes to die, which are highly relevant for ethical debates about end-of-life care and physician-assisted dying. In this reply, we wish to stress the importance of acknowledging and analyzing the sociopolitical context of the phenomenon “being a burden” in relation to wishes to die and we will show how this analysis could benefit from a care ethical approach. As discussions in care ethics have made clear, caring practices are both social and political practices. An empirical and ethical analysis of “being a burden” therefore needs to take institutional and societal norms and structures into account, in addition to first-person experiences and concepts such as caring needs, relational autonomy, and interdependency. Besides the relevance of the sociopolitical context for the phenomenon “being a burden” as such, the sociopolitical context also seems relevant for the investigation of the phenomenon, which we will illustrate by reflecting on “being a burden” in relation to the practice of physician-assisted dying in the Netherlands.     

Epigenetics: localizing biology through co-laboration

This paper reports on a co-laborative laboratory ethnography in a molecular biology laboratory conducting research on environmental epigenetics. It focuses on a single study concerned with the material implications of social differentiation. The analysis briefly raises biopolitical concerns. Its main concern lies with an understanding of the human body as local in its working infrastructure or “inner laboratory”, an understanding that emerges from the co-laborative inquiry between biologists and anthropologist. This co-laborative mode of inquiry raises productive tensions within biology as to the universal or local nature of human nature and within anthropology as to the status of human biology within social theory. The paper cannot resolve this tension. Rather it explores it as an epistemic object in the context of interdisciplinarity, ontography and co-laboration. In concluding, it specifies co-laboration as temporary, non-teleological joint epistemic work aimed at producing new kinds of reflexivity.     

Translational Epigenetics: Clinical Approaches to Epigenome Therapeutics for Cancer

Cancer epigenetics research is now entering an exciting phase of translational epigenetics whereby novel epigenome therapeutics is being developed for application in clinical settings. Epigenetics refers to all heritable and potentially reversible changes in gene or genome functioning that occurs without altering the nucleotide sequence of the DNA. A range of different epigenetic “marks” can activate or repress gene expression. While epigenetic alterations are associated with most cancers, epigenetic dysregulation can also have a causal role in cancer etiology. Epigenetically disrupted stem or progenitor cells could have an early role in neoplastic transformations, while perturbance of epigenetic regulatory mechanisms controlling gene expression in cancer-relevant pathways will also be a contribution factor. The reversibility of epigenetic marks provides the possibility that the activity of key cancer genes and pathways can be regulated as a therapeutic approach. The growing availability of a range of chemical agents which can affect epigenome functioning has led to a range of epigenetic-therapeutic approaches for cancer and intense interest in the development of second-generation epigenetic drugs (epi-drugs) which would have greater specificity and efficacy in clinical settings. The latest developments in this exciting arena of translational cancer epigenetics were presented at a recent conference on “Epigenetics and New Therapies in Cancer” at the Spanish National Cancer Research Center (CNIO), Spain.     

Threads that Guide or Ties that Bind: William Kirby and the Essentialism Story

Nineteenth-century British entomologist William Kirby is best known for his generic division of bees based on tongues and his vigorous defence of natural theology. Focusing on these aspects of Kirby’s work has lead many current scholars to characterise Kirby as an “essentialist.” As a result of this characterisation, many important aspects of his work, Monographia Apum Angliæ (1802) have been over-looked or misunderstood. Kirby’s religious devotion, for example, have lead some scholars to assume Kirby used the term “type” for connecting an ontological assumption about essences with a creationist assumption about species fixity, which I argue conceals a variety of ways Kirby employed the term. Also, Kirby frequently cautioned against organising a classification system exclusively by what he called “analytic reasoning,” a style of reasoning 20th century scholars often associate with Aristotelian logic of division. I argue that Kirby’s critique of analytic reasoning brought the virtues of his own methodological agenda into sharp relief. Kirby used familiar metaphors in the natural history literature – Ariadne’s thread, the Eleusinian mysteries, and Bacon’s bee and spider metaphors – to emphasise the virtues of building tradition and cooperation in the goals and methodological practices of 19th century British naturalists.     

Deconstructing the long-standing a priori assumption that serial homology generally involves ancestral similarity followed by anatomical divergence

It has long been assumed that serial homologues are ancestrally similar—polysomerism resulting from a “duplication” or “repetition” of forms—and then often diverge—anisomerism, for example, as they become adapted to perform different tasks as is the case with the forelimb and hind limbs of humans. However, such an assumption, with crucial implications for comparative, evolutionary, and developmental biology, and for evolutionary developmental biology, has in general not really been tested by a broad analysis of the available empirical data. Perhaps not surprisingly, more recent anatomical comparisons, as well as molecular knowledge of how, for example, serial appendicular structures are patterned along with different anteroposterior regions of the body axis of bilateral animals, and how “homologous” patterning domains do not necessarily mark “homologous” morphological domains, are putting in question this paradigm. In fact, apart from showing that many so-called “serial homologues” might not be similar at all, recent works have shown that in at least some cases some “serial” structures are indeed more similar to each other in derived taxa than in phylogenetically more ancestral ones, as pointed out by authors such as Owen. In this article, we are taking a step back to question whether such assumptions are actually correct at all, in the first place. In particular, we review other cases of so-called “serial homologues” such as insect wings, arthropod walking appendages, Dipteran thoracic bristles, and the vertebrae, ribs, teeth, myomeres, feathers, and hairs of chordate animals. We show that: (a) there are almost never cases of true ancestral similarity; (b) in evolution, such structures—for example, vertebra—and/or their subparts—for example, “transverse processes”—many times display trends toward less similarity while in many others display trends toward more similarity, that is, one cannot say that there is a clear, overall trend to anisomerism.